title: Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions.
abstract: BACKGROUND
  Soybean is an important crop that provides valuable proteins and oils for human use. Because soybean growth and development is extremely sensitive to water deficit, quality and crop yields are severely impacted by drought stress. In the face of limited water resources, drought-responsive genes are therefore of interest. Identification and analysis of dehydration- and rehydration-inducible differentially expressed genes (DEGs) would not only aid elucidation of molecular mechanisms of stress response, but also enable improvement of crop stress tolerance via gene transfer. Using Digital Gene Expression Tag profiling (DGE), a new technique based on Illumina sequencing, we analyzed expression profiles between two soybean genotypes to identify drought-responsive genes.
  
  
  RESULTS
  Two soybean genotypes - drought-tolerant Jindou21 and drought-sensitive Zhongdou33 - were subjected to dehydration and rehydration conditions. For analysis of DEGs under dehydration conditions, 20 cDNA libraries were generated from roots and leaves at two different time points under well-watered and dehydration conditions. We also generated eight libraries for analysis under rehydration conditions. Sequencing of the 28 libraries produced 25,000-33,000 unambiguous tags, which were mapped to reference sequences for annotation of expressed genes. Many genes exhibited significant expression differences among the libraries. DEGs in the drought-tolerant genotype were identified by comparison of DEGs among treatments and genotypes. In Jindou21, 518 and 614 genes were differentially expressed under dehydration in leaves and roots, respectively, with 24 identified both in leaves and roots. The main functional categories enriched in these DEGs were metabolic process, response to stresses, plant hormone signal transduction, protein processing, and plant-pathogen interaction pathway; the associated genes primarily encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significantly expressed (|log2 ratio| ≥ 8) genes - Glyma15g03920, Glyma05g02470, Glyma15g15010, Glyma05g09070, Glyma06g35630, Glyma08g12590, and Glyma11g16000 - are more likely to determine drought stress tolerance. The expression patterns of eight randomly-selected genes were confirmed by quantitative RT-PCR; the results of QRT-PCR analysis agreed with transcriptional profile data for 96 out of 128 (75%) data points.
  
  
  CONCLUSIONS
  Many soybean genes were differentially expressed between drought-tolerant and drought-sensitive genotypes. Based on GO functional annotation and pathway enrichment analysis, some of these genes encoded transcription factors, protein kinases, and other regulatory proteins. The seven most significant DEGs are candidates for improving soybean drought tolerance. These findings will be helpful for analysis and elucidation of molecular mechanisms of drought tolerance; they also provide a basis for cultivating new varieties of drought-tolerant soybean.
authors.affiliation: Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan 430062, China. zhouocri@sina.com.
authors.forename: Li M
authors.initials: LM
authors.lastname: Chen
authors.forename: Xin A
authors.initials: XA
authors.lastname: Zhou
authors.forename: Wen B
authors.initials: WB
authors.lastname: Li
authors.forename: Wei
authors.initials: W
authors.lastname: Chang
authors.forename: Rong
authors.initials: R
authors.lastname: Zhou
authors.forename: Cheng
authors.initials: C
authors.lastname: Wang
authors.forename: Ai H
authors.initials: AH
authors.lastname: Sha
authors.forename: Zhi H
authors.initials: ZH
authors.lastname: Shan
authors.forename: Chan J
authors.initials: CJ
authors.lastname: Zhang
authors.forename: De Z
authors.initials: DZ
authors.lastname: Qiu
authors.forename: Zhong L
authors.initials: ZL
authors.lastname: Yang
authors.forename: Shui L
authors.initials: SL
authors.lastname: Chen
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D016000:Cluster Analysis; D003681:Dehydration; D055864:Droughts; D004553:Electric Conductivity; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D020043:Genes, Essential; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics; D013025:Glycine max / Q000235:genetics* / Q000502:physiology*; D014158:Transcription, Genetic; D014867:Water
chemical_list: D010940:Plant Proteins; D014867:Water